Automatically load volumes that are copied into a folder

This example shows how to implement a simple background task by using a timer. The background task is to check for any new volume files in folder and if there is any then automatically load it.

There are more efficient methods for file system monitoring or exchanging image data in real-time (for example, using OpenIGTLink), the example below is just for demonstration purposes.

incomingVolumeFolder = "c:/tmp/incoming"
incomingVolumesProcessed = []
def checkForNewVolumes():
# Check if there is a new file in the
from os import listdir
from os.path import isfile, join
for f in listdir(incomingVolumeFolder):
if f in incomingVolumesProcessed:
# this is an incoming file, it was already there
continue
filePath = join(incomingVolumeFolder, f)
if not isfile(filePath):
# ignore directories
continue
logging.info("Loading new file: "+f)
incomingVolumesProcessed.append(f)
slicer.util.loadVolume(filePath)
# Check again in 3000ms
qt.QTimer.singleShot(3000, checkForNewVolumes)
# Start monitoring
checkForNewVolumes()

DICOM

How to access top level tags of DICOM images imported into Slicer? For example, to print the first patient's first study's first series' "0020,0032" field:

How to find similar functions? For this one I searched for "slice intersections" text in the whole slicer source code, found that the function is implemented in Base\QTGUI\qSlicerViewersToolBar.cxx, then translated the qSlicerViewersToolBarPrivate::setSliceIntersectionVisible(bool visible) method to Python.

Manipulating objects in the slice viewer

How to define/edit a circular region of interest in a slice viewer?

Drop two markup points on a slice view and copy-paste the code below into the Python console. After this, as you move the markups you’ll see a circle following the markups.

Set slice position and orientation from 3 markup fiducials

Drop 3 markup points in the scene and copy-paste the code below into the Python console. After this, as you move the markups you’ll see the red slice view position and orientation will be set to make it fit to the 3 points.

Set slice position and orientation from a normal vector and position

This code snippet shows how to display a slice view defined by a normal vector and position in an anatomically sensible way: rotating slice view so that "up" direction (or "right" direction) is towards an anatomical axis.

Export a tract (FiberBundle) to Blender, including color

Note: an interactive version of this script is now included in the SlicerDMRI extension (module code).
After installing SlicerDMRI, go to Modules -> Diffusion -> Import and Export -> Export tractography to PLY (mesh).

The example below shows how to export a tractography "FiberBundleNode" to a PLY file:

Modify voxels in a volume

Typically the fastest and simplest way of modifying voxels is by using numpy operators. Voxels can be retrieved in a numpy array using the `array` method and modified using standard numpy methods. For example, threshold a volume:

Get the values of all voxels for a label value

If you have a background image called ‘Volume’ and a mask called ‘Volume-label’ created with the Editor you could do something like this:

import numpy
volume = array(‘Volume’)
label = array(‘Volume-label’)
points = numpy.where( label == 1 ) # or use another label number depending on what you segmented
values = volume[points] # this will be a list of the label values
values.mean() # should match the mean value of LabelStatistics calculation as a double-check
numpy.savetxt(‘values.txt’, values)

Access values in a DTI tensor volume

This example shows how to access individual tensors at the voxel level.

Make mouse left-click and drag on the image adjust window/level

In older Slicer versions, by default, left-click and drag in a slice view adjusted window/level of the displayed image. Window/level adjustment is now a new mouse mode that can be activated by clicking on its toolbar button or running this code:

Save a series of images from a Slice View

You can use ScreenCapture module to capture series of images. To do it programmatically, save the following into a file such as '/tmp/record.py' and then in the slicer python console type "execfile('/tmp/record.py')"

Set up custom units in slice view ruler

For microscopy or micro-CT images you may want to switch unit to micrometer instead of the default mm. To do that, 1. change the unit in Application settings / Units and 2. update ruler display settings using the script below (it can be copied to your Application startup script):

If it is not necessary to preserve file paths then the simplest is to configure default storage node (as shown in the example above), then delete all existing storage nodes. When save dialog is opened, default storage nodes will be recreated.

# Delete existing model storage nodes so that they will be recreated with default settings
existingModelStorageNodes = slicer.util.getNodesByClass('vtkMRMLModelStorageNode')
for modelStorageNode in existingModelStorageNodes:
slicer.mrmlScene.RemoveNode(modelStorageNode)

To update existing storage nodes to use new file extension (but keep all other parameters unchanged) you can use this approach (example is for volume storage):

Show a segmentation in 3D

Segmentation can only be shown in 3D if closed surface representation (or other 3D-displayable representation) is available. To create closed surface representation:

segmentation.CreateClosedSurfaceRepresentation()

Get a representation of a segment

Access binary labelmap stored in a segmentation node (without exporting it to a volume node) - if it does not exist, it will return None:

image = segmentationNode.GetBinaryLabelmapRepresentation(segmentID)

Get closed surface, if it does not exist, it will return None:

polydata = segmentationNode.GetClosedSurfaceRepresentation(segmentID)

Get binary labelmap representation. If it does not exist then it will be created for that single segment. Applies parent transforms by default (if not desired, another argument needs to be added to the end: false):

How to run segment editor effects from a script

Editor effects are complex because they need to handle changing master volumes, undo/redo, masking operations, etc. Therefore, instead of using a segment editor effect, it is simpler to run the underlying filters directly from script.

This example demonstrates how to use Segment editor effects (without GUI, using qMRMLSegmentEditorWidget):

Get the pseudo-singleton subject hierarchy node

Create subject hierarchy item

# If it is for a data node, it is automatically created, but the create function can be used to set parent:
shNode.CreateItem(parentItemID, dataNode)
# If it is a hierarchy item without a data node, then the create function must be used:
shNode.CreateSubjectItem(parentItemID, name)
shNode.CreateFolderItem(parentItemID, name)
shNode.CreateHierarchyItem(parentItemID, name, level) # Advanced method to set level attribute manually (usually subject, study, or folder, but it can be a virtual branch for example)

Using matplotlib

Matplotlib may be used from within Slicer, but the default Tk backend locks up and crashes Slicer. However, Matplotlib may still be used through other backends. More details can be found on the MatPlotLib pages.

Execute external applications

How to run external applications from Slicer.

Run process in default environment

When a process is launched from Slicer then by default Slicer's ITK, VTK, Qt, etc. libraries are used. If an external application has its own version of these libraries, then the application is expected to crash. To prevent crashing, the application must be run in the environment where Slicer started up (without all Slicer-specific library paths). This startup environment can be retrieved using slicer.util.startupEnvironment().